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H2BC4 H2B clustered histone 4 [ Homo sapiens (human) ]

Gene ID: 8347, updated on 10-Dec-2024

Summary

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Official Symbol
H2BC4provided by HGNC
Official Full Name
H2B clustered histone 4provided by HGNC
Primary source
HGNC:HGNC:4757
See related
Ensembl:ENSG00000180596 MIM:602847; AllianceGenome:HGNC:4757
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
H2B.1; H2B/l; H2BC6; H2BC7; H2BC8; H2BFL; H2BC10; HIST1H2BC; dJ221C16.3
Summary
Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. The protein has antibacterial and antifungal antimicrobial activity. The main transcript variant of this gene is intronless and encodes a replication-dependent histone that is a member of the histone H2B family. This transcript variant lacks a polyA tail but instead contains a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6. [provided by RefSeq, Apr 2020]
Orthologs
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Genomic context

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See H2BC4 in Genome Data Viewer
Location:
6p22.2
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (26113170..26123926, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (25981318..25992074, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (26113398..26124154, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:26103833-26104523 Neighboring gene H4 clustered histone 3 Neighboring gene H1.6 linker histone, cluster member Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:26121574-26122260 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:26122261-26122945 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:26123079-26124278 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:26124310-26125509 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24192 Neighboring gene H2A clustered histone 6 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:26156285-26157036 Neighboring gene H1.4 linker histone, cluster member

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. A subset of replication-dependent histone mRNAs are expressed as polyadenylated RNAs in terminally differentiated tissues. Lyons SM, et al. Nucleic Acids Res, 2016 Nov 2. PMID 27402160, Free PMC Article
  2. Human spleen histone H2B. Isolation and amino acid sequence. Ohe Y, et al. J Biochem, 1979 Feb. PMID 422550
  3. The structural basis of modified nucleosome recognition by 53BP1. Wilson MD, et al. Nature, 2016 Aug 4. PMID 27462807
  4. Chromosomes. CENP-C reshapes and stabilizes CENP-A nucleosomes at the centromere. Falk SJ, et al. Science, 2015 May 8. PMID 25954010, Free PMC Article
  5. Multivalent DNA and nucleosome acidic patch interactions specify VRK1 mitotic localization and activity. Budziszewski GR, et al. Nucleic Acids Res, 2022 May 6. PMID 35390161, Free PMC Article

See all (66) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Histone H2B antimicrobial peptides participate in the colonic defense against bacteria and fungi.
    Title: Antimicrobial peptides in the first line defence of human colon mucosa.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association meta-analysis for total serum bilirubin levels.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of histone cluster 1, H2bc (HIST1H2BC) by siRNA enhances the early stages of HIV-1 replication in HeLa-CD4 cells infected with viral pseudotypes HIV89.6R and HIV8.2N PubMed

Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev interacting protein, histone cluster 1, H2bc, is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells PubMed
Tat tat HIV-1 Tat peptides bind core histones H2A, H2B, H3 and H4, and Tat protein recruits histone acetyltransferases to the HIV-1 LTR promoter leading to acetylation of histones H3 and H4, derepressing chromatin structure and increasing NFkappaB responsiveness PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC104246

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding NAS
Non-traceable Author Statement
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein heterodimerization activity IEA
Inferred from Electronic Annotation
more info
  
enables structural constituent of chromatin IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in antibacterial humoral response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in antimicrobial humoral immune response mediated by antimicrobial peptide IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in defense response to Gram-positive bacterium IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in innate immune response in mucosa IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in nucleosome assembly NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in extracellular exosome HDA PubMed 
located_in extracellular space IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
part_of nucleosome NAS
Non-traceable Author Statement
more info
 PubMed 
located_in nucleus HDA PubMed 

General protein information

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Preferred Names
histone H2B type 1-C/E/F/G/I
Names
H2B histone family, member L
histone 1, H2bc
histone H2B.1 A
histone H2B.l
histone cluster 1 H2B family member c
histone cluster 1, H2bc

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001381989.1 → NP_001368918.1  histone H2B type 1-C/E/F/G/I

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
    Source sequence(s)
    U91328
    Consensus CDS
    CCDS4584.1
    UniProtKB/Swiss-Prot
    P02278, P62807, Q3B872, Q4VB69, Q93078, Q93080
    UniProtKB/TrEMBL
    B2R4S9, Q0D2M2
    Related
    ENSP00000321744.4, ENST00000314332.5
    Conserved Domains (1) summary
    smart00427
    Location:28 → 124
    H2B; Histone H2B

  2. NM_003526.3 → NP_003517.2  histone H2B type 1-C/E/F/G/I

    See identical proteins and their annotated locations for NP_003517.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
    Source sequence(s)
    U91328
    Consensus CDS
    CCDS4584.1
    UniProtKB/Swiss-Prot
    P02278, P62807, Q3B872, Q4VB69, Q93078, Q93080
    UniProtKB/TrEMBL
    B2R4S9, Q0D2M2
    Related
    ENSP00000380180.1, ENST00000396984.2
    Conserved Domains (1) summary
    smart00427
    Location:28 → 124
    H2B; Histone H2B

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    26113170..26123926 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    25981318..25992074 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P62807.4 GenPept UniProtKB/Swiss-Prot:P62807

Gene LinkOut

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